Dukat's Bird-of-Prey breaks off from the Defiant and starts to follow the Dominion fleet. Kira, thinking Dukat is trying to be a hero, tells him to stop but Dukat clarifies that he isn't chasing the fleet... he's joining it. He then reveals a startling fact; over the last few months, he has been conducting secret negotiations and, as of a week earlier, the Cardassian Union are officially members of the Dominion. He then bids farewell to Kira, wryly noting that the two of them being on the same side never seemed right. He then makes a getaway before the Defiant can destroy his ship.

Worf, Bashir, Garak, and Martok plan their escape from Internment Camp 371. The prisoners in Internment Camp 371 are gathered together. The prison's commanding Vorta, Deyos, announces that Cardassia has joined the Dominion and, consequently, all the Cardassians imprisoned at 371 are being released... with the exception of Garak. When Garak demands to know why he is not being released, Deyos reveals that the new head of the Cardassian government is none other than Gul Dukat.

Dukat soon makes his first broadcast as leader to the people of Cardassia, while Sisko and the others watch on DS9. Dukat promises to remove all Klingons and Maquis from within Cardassian space, as well as anyone else who gets in the way of Cardassia's return to a position of prominence in the Alpha Quadrant.

The senior staff discuss the situation. The wormhole's entrance, rather than being sealed, has now been strengthened to the point that it can never be collapsed. Between this and the sudden disappearance of an engineering officer, Changeling involvement is suggested by none other than by the Julian BashirChangeling. With this, he is authorized to begin blood screenings.

While Garak works inside a tight space next to their cell to contact their runabout's transporter, Worf is coerced into a series of hand-to-hand battles with Jem'Hadar warriors, beginning with the youngest.

Back in the Alpha Quadrant, Kira and Ziyal talk on the Promenade, discussing the duplicitous actions of her father, Dukat.

A battered Klingon fleet led by ChancellorGowron unexpectedly arrives at DS9 - the newly arrived Dominion fleet has quickly turned the tide of the Klingon-Cardassian War in favor of the Cardassians, and the incensed Gowron is ready to plunge the Klingon Empire into a fight to the death with the Dominion. Sisko suggests to Gowron that the Khitomer Accords be revived for the sake of bolstering their forces for the coming conflict. Gowron accedes. Afterwards, the Bashir Changeling successfully sneaks aboard the runabout USS Yukon and starts making modifications.

Worf continues fighting the Jem'Hadar and kills the last one of five, earning awe and admiration from Martok. Once back in the cell, Bashir treats Worf and states that he has three or four broken ribs. The Doctor recommends that Worf stop fighting, but Worf refuses.

Garak is still working inside the tight space, talking to himself, and seems to be losing his mind. The others hear strange noises coming from within the space. When the Jem'Hadar guards pass the cell, the prisoners hurriedly shut off the power, plunging the enclosed space into darkness. When the guards have gone, Bashir enters the space and pulls Garak out. For the next several hours, he lies on his bunk, unmoving, staring straight ahead. Bashir grimly states that Garak's claustrophobia has overcome him, and they will be unable to try contacting the runabout.

The staff aboard DS9 is waiting for reinforcements. Kira enters Ops and states that the security blocks of one of the industrial replicators was overridden and the memory core wiped. Benjamin Sisko is contacted by Gul Dukat, who has been declared the head of the new Cardassian government. Dukat recommends that the Federation join the Dominion. Dukat lays claim to DS9 and gives Sisko an ultimatum: either Sisko will surrender the station, or Dukat will take it by force.

Martok assists Worf back to the cell, returning from his seventh hand-to-hand victory. Bashir patches him up as best as he can, wryly asking Martok to include a mention of him in the epic song he will compose about Worf's battles. Martok laughs and states that Bashir's work has earned him several verses, at the very least. Becoming serious, Bashir says that Worf is supposed to be buying them time, but with Garak out of action, they have no way of completing his work, though Bashir is willing to try.

To everyone's surprise, Garak rises from his bunk and cheerfully says that won't be necessary; he's rested enough, and it's time for him to get back to work inside his "dungeon". As he ducks into the cramped space again, the two Klingon warriors look on with respect, both of them knowing that it takes true courage to face one's own worst fears.

The Julian Bashir Changeling and O'Brien talk in the infirmary. O'Brien is shocked when Bashir talks excitedly about having purchased duridium alloy darts at a time like this, but does not suspect that Bashir is a Changeling.

Worf, back at the combat area, is waiting for his next opponent, when Deyos and the Jem'Hadar First, Ikat'ika, arrive instead. Ikat'ika announces that he will fight Worf himself.

Meanwhile, Garak is back in the crawlspace when Jem'Hadar soldiers come in the cell looking for him. They find the tool that was used to open the panel to the space where Garak is.

Sisko orders Kira and Dax to the Defiant for the pending battle and deploys the runabouts. The Julian Bashir Changeling is on the runabout Yukon and responds to Ops in a female voice, having already incapacitated the original crew. O'Brien announces that a build up of tachyon particles has been detected, and ships begin decloaking around the station... Romulan ships. The Romulans request permission to join the fleet; Sisko, while quite surprised, grants their request.

Kira, on the Defiant, states that the Cardassian-Dominion fleet is merely ten minutes away.

Bashir tries to bluff the Jem'Hadar soldier about the tool. Bashir flippantly quips that "it's either a self-sealing stem bolt or a reverse-ratcheting router". Not convinced, the soldier vaporizes a Romulan prisoner and then threatens to kill another if Bashir continues to lie. Before the leader can kill Bashir for his insolence, another soldier figures out the tool's use.

In the ring, Worf is losing the fight against Ikat'ika, and can barely stand. When he is knocked down yet again, Martok urges him to yield, insisting that "honor has been satisfied."

Garak is perilously close to being found out when a Breen prisoner grabs the plasma pistol from the holster of a Jem'Hadar who had his back turned, and vaporizes two of the guards, though the second manages to vaporize him as well. Bashir and the Romulan prisoner kill the remaining guards with makeshift knives, and grab their weapons, urging Garak to complete his work before Jem'Hadar reinforcements storm into the cell.

In the ring, Worf is clearly beaten, but still refuses to yield. As he crawls on his belly towards the post, even Ikat'ika tries to dissuade him from continuing, saying that Worf has earned the respect of everyone there. But Worf still refuses to yield, and Deyos impatiently orders the combat finished. To everyone's surprise, Ikat'ika instead steps back and yields the match, announcing that he may be able to kill Worf, but he cannot defeat him. Irritated, Deyos orders them both executed.

Just as the guards raise their weapons, Garak succeeds in activating his makeshift communicator, and the runabout immediately energizes its transporter, beaming all the prisoners away; as the guards open fire, Ikat'ika is vaporized by a plasma bolt, but Worf is beamed away a split second before the weapons fire impacts him.

Aboard the runabout, Garak immediately lays in an escape course, while Martok and Bashir help a badly-injured Worf back to the sickbay. Before going, Worf makes sure to tell the Cardassian that he "did well," and Garak returns the compliment. The crew then set a course back to the station at maximum warp.

Back on DS9, everyone is confused by the lack of an attacking fleet contrary to the sensor readings. Suddenly, they get a hail from the real Bashir in the Gamma Quadrant. Sisko quickly realizes that the Bashir they've been dealing with was the Changeling and quickly discerns that he left aboard the runabout Yukon. He then orders Kira aboard the USS Defiant to destroy the runabout at no matter the cost.

Kira and Dax determine that the Changeling has rigged the Yukon with trilithium, tekasite, and protomatter, which if detonated inside the Bajoran sun, would induce a supernova, destroying Bajor, DS9, and the Klingon, Romulan, and Federation fleets in one fell swoop. The Defiant warps toward the sun and tractors the Yukon away in time to prevent the supernova. It dives off into free space and explodes, killing the Changeling and incapacitated crew still aboard.

The sensor readings of the Dominion fleet suddenly vanish. Sisko realizes that the whole incident was a plot to lure the combined fleets of the Alpha Quadrant's superpowers to the Bajoran system and then blow them all up together with Bajor and Deep Space 9. Yet the plan failed and "Armageddon will have to wait... for another day".

At Quark's, Garak and Ziyal emotionally reunite, as do Dax and Worf in the infirmary. Meanwhile, Chief O'Brien is baffled to realize he has been hanging around with a Changeling for the last four weeks.

On the Promenade, Gowron signs the final version of the new treaty between the Federation and the Klingon Empire, which includes a permanent Klingon military presence on DS9. Sisko is given the right to choose the commander himself, and considering Worf and Martok's mutual admiration, he asks the general to do the job, which he gladly accepts.

Dukat contacts Sisko to congratulate him. Sisko points out that Ziyal would have died along with them if the bomb had gone off, but the new leader of Cardassia does not seem to be bothered, saying he no longer considers her his daughter. Dukat tells Sisko that he may have escaped defeat today, but tomorrow... "We will see about tomorrow", the captain interrupts.

"For the past few months, I've been conducting secret negotiations between the Dominion and Cardassia. And, as of last week, Cardassia has agreed to become part of the Dominion."

- Dukat, to Major Kira

"I am pleased to announce that hostilities between our peoples have ended. As of today, Cardassia has joined the Dominion. Therefore, you are all being sent home. Congratulations on your new status as Dominion citizens."

- Deyos, to the Cardassian prisoners

"The last time I checked, I was a Cardassian."
"But not a very popular one, I'm afraid. At least not with the head of the new Cardassian government."
"And who would that be?"
"Gul Dukat."

- Garak and Deyos

"You might ask: Should we fear joining the Dominion? And I answer you: Not in the least. We should embrace the opportunity. The Dominion recognizes us for what we are: the true leaders of the Alpha Quadrant. And now that we are joined together, equal partners in all endeavors, the only people with anything to fear will be our enemies."

- Gul Dukat

"My oldest son's birthday is in five days. To him and to Cardassians everywhere, I make the following pledge: By the time his birthday dawns, there will not be a single Klingon alive inside Cardassian territory. Or a single Maquis colony left within our borders."

- Gul Dukat

"Cardassia will be made whole. All that we have lost will be ours again. And anyone who stands in our way will be destroyed. This I vow with my life's blood. For my son, for all our sons."

- Gul Dukat

"Today, we train against a worthy adversary. Observe. Analyze. Remember. Soon, we will face his people in combat. The lessons you learn here will ensure victory. Victory is life!!"

- Ikat'ika

"Think of it. Five years ago, no one had ever heard of Bajor or Deep Space 9 and now...all our hopes rest here. Where the tides of fortune take us, no man can know."
"They're tricky, those tides."

- Gowron and Sisko

"Dukat, if you have something to say to me, say it!"
"Then I'll make it simple. A few days ago, I swore all Cardassia lost would be regained. That space station you're so fond of was built by Cardassia."
"Funny. I thought it was built by Bajoran slave labor."

- Sisko and Dukat, on Deep Space 9

"Either surrender the station, or I'll take it by force. The choice is yours."
"If you want to retake the station, Dukat, you're welcome to try."

- Gul Dukat and Sisko, on Deep Space 9

"The Jem'Hadar don't eat, don't drink and they don't have sex... and if that wasn't bad enough, the Founders don't eat, don't drink and they don't have sex either, which, between you and me, makes my financial future less than promising."
"It might not be so bad. For all we know the Vorta could be gluttonous, alcoholic sex maniacs."

- Quark and Tora Ziyal

"Tell our friends out there to stand down. Armageddon will have to wait for another day."

"Tain, I don't know if you can hear me, but if you can, I just want you to know, you may not have been much of a father, but I really wish you were alive right now. That way, you could be in here, instead of me."

- Garak

"There is no greater enemy than one's own fears."
"It takes a brave man to face them."

- Martok and Worf, as Garak returns to work in his "dungeon."

"My people have a saying: 'Never turn your back on a Breen.'"

- The female Romulan prisoner, about the Breen prisoner

"You fight because that is what you were designed to do. All that motivates him is some barbaric sense of honor."
"And that is something you will never understand."

- Deyos and Ikat'ika, on Worf

"Victory is life."
"Today is a good day to die."

- Ikat'ika and Worf, comparing worldviews

"Four weeks? Are you telling me I've been hanging around with a Changeling for over a month?"
"And you even never suspected it wasn't me?"
"No! And the worst part is, the clues were right in front of me!"
"What clues?"
"Well, for one thing, he was a lot easier to get along with."

- O'Brien and Bashir

"I yield. I cannot defeat this Klingon. All I can do is kill him. And that no longer holds my interest."

- Ikat'ika, when Worf refuses to stay down

"Right now I wouldn't believe your father if he said rain was wet."

- Kira Nerys, to Tora Ziyal

"I'm sorry, but that's absolutely unacceptable! I'm under enough strain as it is - I can't have you quitting on me!"

- Garak talking to a failing light, trying to control his claustrophobia

"What I did, I did to make Cardassia strong again. And mark my words, Captain, I've succeeded. You may have escaped defeat this day, but tomorrow..."
"We will see about tomorrow."
"Yes, we will."

This episode ends the process of depicting the character of Gul Dukat in a more sympathetic light, a process which began in "The Maquis, Part II" and was carried on in episodes such as "Civil Defense", "Defiant", "The Way of the Warrior", "Indiscretion", "Return to Grace", and "Apocalypse Rising". Ever since "The Maquis, Part II", Dukat's role as a clear-cut villain had been rendered more and more ambiguous, especially in the aforementioned three episodes from the fourth season. Whereas the character had initially been introduced as a typical bad guy, it seemed that the writers were on course to completely turn him around, and eventually have him as a protagonist. However, according to both Ira Steven Behr and Robert Hewitt Wolfe, they had always intended Dukat's change of heart to be temporary, and they always knew, even when writing episodes like "Defiant", that somewhere down the road he would show everybody just how truly evil he really was. As Behr explains, they never had any intention of turning Dukat into a good guy; "Dukat is a self-deluded, opportunistic, egomaniacal sadist. In other words he is the Richard Nixon of Deep Space Nine. He will do whatever it takes to come out on top." (Star Trek: Deep Space Nine Companion)

Regarding how the transporter identified the escapees, Ronald D. Moore commented: "I think that Garak programmed the transporter to beam out anyone who wasn't a Jem'Hadar or a Vorta within a given area." (AOL chat,1997)

Although both this episode and "In Purgatory's Shadow" were extremely popular with viewers, the producers were a little disappointed with how the two-parter turned out. As Ira Steven Behr explains, "I'm not sure if this worked as well as it could have as a two-parter. It might have been better as a two-hour block. Or even as a ninety-minute show. We didn't really gain anything by splitting them up. The second hour moves like a house on fire. Events are happening at such an accelerated pace. If we'd had the hour or forty-five-minute buildup immediately precede it, I'd have liked it better." (Star Trek: Deep Space Nine Companion)

This episode marks the second time that Bashir has been replaced by a Changeling, the first being "The Adversary".

There are a great number of references to previous episodes: Worf's desire to fight a Jem'Hadar, as revealed in "To the Death", is here realized; the Dominion fleet heading towards Bajor but then turning and moving towards Cardassia confirms Sisko's vision of locusts in "Rapture"; Dukat's reference to himself and Kira being on the same side refers to "Indiscretion" and "Return to Grace"; the references to Cardassian cultural depression and economic stagnation, and Dukat's promise to eliminate all Klingon troops in Cardassian territory, recalls the events of "The Way of the Warrior"; Dukat's reference to Sisko saving his life more than once refers to the episodes "The Maquis, Part II", where Sisko rescues Dukat from the Maquis, and "The Way of the Warrior", in which Sisko helps Dukat escape Cardassia before the Klingon fleet arrives.

Dukat's line to Ziyal at the end of "In Purgatory's Shadow", "stay here and be damned!", paralleled Kang in "Blood Oath". This episode reveals that, like Kang, he was hiding the fact that he was collaborating with the enemy. Unlike Kang, he does not redeem himself in the remaining hour.